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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
feat(qc-metrics): add common single cell quality control metrics
…ial transcriptomics quality control metrics
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
…istics function and tests based on the PR review
feat(qc_summary_statistics): add summary statistics table for sc/spatial transcriptomics quality control metrics
…plate feat(visualize_ripley_template): add visualize_ripley_template and un…
Refactor: template-utils with review fixes
…anch and fix unit test
fix(ripley_template): address review comments - replace debug prints …
…port - Add load_csv_files() to template_utils.py for loading and combining CSV files - Add spell_out_special_characters() to handle biological marker names - Add load_csv_files_with_config.py template wrapper for NIDAP compatibility - Add comprehensive unit tests for both functions - Support column name cleaning, metadata mapping, and string column enforcement
feat: add spac_load_csv, spac_arcsinh_normalization, spac_interactive_spatial_plot galaxy tools
feat: add galaxy tools spac_setup_analysis and updated spac_boxplot with correct json outputs and validated h5ad intake.
feat: add spac_zscore_normalization galaxy tools
refactor: streamline galaxy tools implementation
feat: add refactored galaxy tools
Benchmark script
fix(nearest_neighbor_template): Break the title in two lines
- Refactored all template run_from_json() functions to use centralized save_results from template_utils - Added show_static_image toggle (default False) to relational_heatmap_template and sankey_plot_template to prevent Plotly-to-PNG hang on Galaxy - Refactored all unit tests in tests/templates/ using snowball approach: real data, real filesystem, no mocking - One test file per template validating output file existence, naming conventions, and non-empty artifacts - Updated posit_it_python_template to use centralized save_results Templates changed: 43 files in src/spac/templates/ Tests changed: 37 files in tests/templates/
- test_boxplot_performance.py - test_histogram_performance.py
refactor all templates and unit tests
…plates fix: Remove 6 deprecated templates (sync with tools_refactor)
merge dev to release_dev for updated spac templates
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